Paste your alignment in FASTA format into the field below:

Submit a file in FASTA format directly from your local disk:

At most 3000 sequences per submission; maximal sequence length of 5,000 residues.

The sequences are kept confidential and will be deleted after processing.


Determine valid char set in sequences. Anything not valid is considered a gap.

Delete columns in result if only gaps in column
Detailed output
Ensure optimal solution (costly)

If you want to use a protein alignment but obtain the output in nucleotides, please submit the nucleotide alignment below (you must still submit the protein alignment in the field on the top of the page).
The fasta identifiers for every sequence must be identical in the two alignments.

Submit a second fasta file in FASTA format directly from your local disk:


For publication of results, please cite:

MaxAlign: maximizing usable data in an alignment
BMC Bioinformatics 2007, 8:312
Gouveia-Oliveira R, Sackett P W, Pedersen A G

Downloadable Version

Would you prefer to run MaxAlign at your own machine?
MaxAlign 1.1 is available for download. Right-click - Save as.
You need a perl installation to run MaxAlign, but nothing else as the program is made in pure perl and requires no extra modules.